ExxonMobil Biomedical Sciences Incorporated, Annandale, NJ, United States of America.
PLoS One. 2018 Apr 24;13(4):e0196430. doi: 10.1371/journal.pone.0196430. eCollection 2018.
Extracting and identifying genetic material from environmental media (i.e. water and soil) presents a unique opportunity for researchers to assess biotic diversity and ecosystem health with increased speed and decreased cost as compared to traditional methods (e.g. trapping). The heterogeneity of soil mineralogy, spatial and temporal variations however present unique challenges to sampling and interpreting results. Specifically, fate/transport of genetic material in the terrestrial environment represents a substantial data gap. Here we investigate to what degree, benthic fauna transport genetic material through soil. Using the red worm (Eisenia fetida), we investigate how natural movement through artificial soil affect the transport of genetic material. All experiments were run in Frabill® Habitat® II worm systems with approximately 5 cm depth of artificial soil. We selected an "exotic" source of DNA not expected to be present in soil, zebrafish (Danio rerio) tissue. Experiment groups contained homogenized zebrafish tissue placed in a defined location combined with a varying number of worms (10, 30 or 50 worms per experimental group). Experimental groups comprised two controls and three treatment groups (representing different worm biomass) in triplicate. A total of 210 soil samples were randomly collected over the course of 15 days to investigate the degree of genetic transfer, and the rate of detection. Positive detections were identified in 14% - 38% of samples across treatment groups, with an overall detection rate of 25%. These findings highlight two important issues when utilizing environmental DNA for biologic assessments. First, benthic fauna are capable of redistributing genetic material through a soil matrix. Second, despite a defined sample container and abundance of worm biomass, as many as 86% of the samples were negative. This has substantial implications for researchers and managers who wish to interpret environmental DNA results from terrestrial systems. Studies such as these will aid in future study protocol design and sample collection methodology.
从环境介质（如水体和土壤）中提取和鉴定遗传物质，为研究人员提供了一个独特的机会，可以在提高速度和降低成本的情况下，评估生物多样性和生态系统健康状况，与传统方法（如诱捕）相比。然而，土壤矿物学的异质性、时空变化给采样和解释结果带来了独特的挑战。具体来说，遗传物质在陆地环境中的命运/迁移代表了一个实质性的数据空白。在这里，我们研究了底栖动物在多大程度上通过土壤运输遗传物质。我们使用红蚯蚓（Eisenia fetida），研究了自然通过人工土壤的运动如何影响遗传物质的迁移。所有实验均在 Frabill® Habitat® II 蚯蚓系统中进行，人工土壤深度约为 5 厘米。我们选择了一种“外来”的 DNA 来源，预计不会存在于土壤中，即斑马鱼（Danio rerio）组织。实验组包含放置在特定位置的均匀化斑马鱼组织，以及数量不同的蚯蚓（每组实验 10、30 或 50 条蚯蚓）。实验组包括两个对照组和三个处理组（代表不同的蚯蚓生物量），每组重复三次。在 15 天的时间里，共随机采集了 210 个土壤样本，以研究遗传转移的程度和检测率。在处理组中，有 14%至 38%的样本中检测到阳性，总体检测率为 25%。这些发现强调了在利用环境 DNA 进行生物评估时需要考虑两个重要问题。首先，底栖动物能够通过土壤基质重新分配遗传物质。其次，尽管有明确的样本容器和大量的蚯蚓生物量，多达 86%的样本是阴性的。这对希望从陆地系统解释环境 DNA 结果的研究人员和管理者具有重要意义。此类研究将有助于未来研究方案设计和样本采集方法。
